Handel Package

Program list...

• Handel: an evolutionary model-based Statistical Alignment package. Includes:
  • tkfemit - program to sample multiple alignments from the prior implied by the TKF91 model and a given phylogenetic tree
    • Input: tree (Newick Format), optional rate matrix (XrateFormat)
    • Output: alignment (Stockholm Format)
  • tkfdistance - program to estimate distance matrices using the TKF91 model
    • Input: either sequences (Fasta Format) or an alignment (Stockholm Format)
    • Output: distance matrix (Distance Format)
  • tkfalign - MCMC phylogenetic alignment package using TKF91
    • Input: tree (Newick Format), optional rate matrix (XrateFormat), and either sequences (Fasta Format) or an alignment (Stockholm Format)
    • Output: alignment(s) (Stockholm Format)
    • See Why MCMC Is Networking For Modelers for discussion of why the MCMC functionality is cool
  • phylocomposer - program for analysis using String Transducers
    • Input: tree, transducer composition file (Phylo Composer format -- a derivative of Lisp S Expressions)
    • Output: composite & acyclic transducers, alignments (Phylo Composer format)
  • phylodirector.pl - program for visualizing state paths through String Transducers
    • Input: alignment (Stockholm Format)
    • Output: movie file (MPEG Format); still image files (PNG Format & SVG Format)

Related programs in DART...

• Stem Loc, Evol Doer: multiple alignment of RNA
  • Input: either sequences (Fasta Format) or alignments (Stockholm Format)
  • Output: alignment(s) (Stockholm Format)

• xrate: mutation rate measurement using EM algorithm (Xrate Format, Stockholm Format)
• xfold, xprot and xgram: multiple alignment annotation using evolutionary SCFGs (Xgram Format, Stockholm Format)

Background...

• See Phylogenetic Alignment Reader for more background info and context on Phylo Alignment
  • a good review is Lunter G, Miklos I, Drummond A, Jensen JL, Hein J.  Bayesian coestimation of phylogeny and sequence alignment.  BMC Bioinformatics. 2005 Apr 1;6:83.
• See Multiple RNA Alignment for papers and theory relating to multiple alignment of RNA

Getting in touch...

• Dart Mailing Lists
• Dart Release Notes
• Known issues with DART
• Dart Bug Reporting